@article {ellingsrud2021validating,
	title = {Validating a computational framework for ionic electrodiffusion with cortical spreading depression as a case study},
	journal = {eNeuro},
	volume = {9},
	number = {2},
	year = {2022},
	month = {04/2022},
	publisher = {Society for Neuroscience},
	author = {Ada Johanne {Ellingsrud} and Didrik B. {Dukefoss} and Enger, Rune and Halnes, Geir and Pettersen, Klas and Marie E. {Rognes}}
}
@misc {28263,
	title = {Accurate numerical simulation of electrodiffusion and water movement in brain tissue with cortical spreading depression as a case study},
	howpublished = {Interpore 13th annual meeting (online)},
	year = {2021},
	type = {Conference talk},
	address = {Online},
	author = {Ada Johanne {Ellingsrud} and Marie E. {Rognes}},
	editor = {Farrell, Patrick and Boull{\'e}, Nicolas and Didrik B. {Dukefoss} and Enger, Rune and Pettersen, Klas and Halnes, Geir}
}
@misc {28264,
	title = {Finite element simulation of ionic electrodiffusion in cellular geometries},
	howpublished = {Online},
	year = {2020},
	publisher = {29th annual computational neuroscience meeting},
	type = {Conference talk},
	address = {Online},
	author = {Ada Johanne {Ellingsrud} and Marie E. {Rognes}},
	editor = {Halnes, Geir and Solbr{\r a}, Andreas and Einevoll, Gaute}
}
@article {paper30,
	title = {Finite element simulation of ionic electrodiffusion in cellular geometries},
	journal = {Frontiers in Neuroinformatics},
	volume = {14},
	year = {2020},
	pages = {11},
	publisher = {Frontiers},
	doi = {https://doi.org/10.3389/fninf.2020.00011},
	author = {Ada Johanne {Ellingsrud} and Solbraa, Andreas and Gaute T. {Einevoll} and Halnes, Geir and Marie E. {Rognes}}
}
@inbook {23577,
	title = {Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow},
	booktitle = {Computational Glioscience  },
	year = {2019},
	publisher = {Springer},
	organization = {Springer},
	address = {Springer Series in Computational Neuroscience},
	author = {Halnes, Geir and Klas H. {Pettersen} and {\O}yehaug, Leiv and Marie E. {Rognes} and Hans Petter {Langtangen} and Gaute T {Einevoll}},
	editor = {Pitta, D{\'e} and Berry, H.}
}
@article {26194,
	title = {A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons},
	journal = {PLOS Computational Biology},
	volume = {14},
	number = {1-26},
	year = {2018},
	month = {10/2018},
	publisher = {Public Library of Science},
	abstract = {Many pathological conditions, such as seizures, stroke, and spreading depression, are associated with substantial changes in ion concentrations in the extracellular space (ECS) of the brain. An understanding of the mechanisms that govern ECS concentration dynamics may be a prerequisite for understanding such pathologies. To estimate the transport of ions due to electrodiffusive effects, one must keep track of both the ion concentrations and the electric potential simultaneously in the relevant regions of the brain. Although this is currently unfeasible experimentally, it is in principle achievable with computational models based on biophysical principles and constraints. Previous computational models of extracellular ion-concentration dynamics have required extensive computing power, and therefore have been limited to either phenomena on very small spatiotemporal scales (micrometers and milliseconds), or simplified and idealized 1-dimensional (1-D) transport processes on a larger scale. Here, we present the 3-D Kirchhoff-Nernst-Planck (KNP) framework, tailored to explore electrodiffusive effects on large spatiotemporal scales. By assuming electroneutrality, the KNP-framework circumvents charge-relaxation processes on the spatiotemporal scales of nanometers and nanoseconds, and makes it feasible to run simulations on the spatiotemporal scales of millimeters and seconds on a standard desktop computer. In the present work, we use the 3-D KNP framework to simulate the dynamics of ion concentrations and the electrical potential surrounding a morphologically detailed pyramidal cell. In addition to elucidating the single neuron contribution to electrodiffusive effects in the ECS, the simulation demonstrates the efficiency of the 3-D KNP framework. We envision that future applications of the framework to more complex and biologically realistic systems will be useful in exploring pathological conditions associated with large concentration variations in the ECS.},
	doi = {10.1371/journal.pcbi.1006510},
	url = {http://dx.plos.org/10.1371/journal.pcbi.1006510},
	author = {Solbr{\r a}, Andreas and Bergersen, Aslak and van den Brink, Jonas and Malthe-S{\o}renssen, Anders and Gaute T. {Einevoll} and Halnes, Geir},
	editor = {Barreto, Ernest}
}
@article {24994,
	title = {An Evaluation of the Accuracy of Classical Models for Computing the Membrane Potential and Extracellular Potential for Neurons},
	journal = {Frontiers in Computational Neuroscience},
	volume = {11},
	year = {2017},
	pages = {27},
	publisher = {Frontiers Media SA},
	abstract = {Two mathematical models are part of the foundation of Computational neurophysiology; a) the Cable equation is used to compute the membrane potential of neurons, and, b) volume-conductor theory describes the extracellular potential around neurons. In the standard procedure for computing extracellular potentials, the transmembrane currents are computed by means of a) and the extracellular potentials are computed using an explicit sum over analytical point-current source solutions as prescribed by volume conductor theory. Both models are extremely useful as they allow huge simplifications of the computational efforts involved in computing extracellular potentials. However, there are more accurate, though\&nbsp;computationally very expensive, models available where the potentials inside and outside the neurons are computed simultaneously in a self-consistent scheme. In the present work we explore the accuracy of the classical models a) and b) by comparing them to these more accurate schemes.The main assumption of a) is that the ephaptic current can be ignored in the derivation of the Cable equation. We find, however, for our examples with stylized neurons, that the ephaptic current is comparable in magnitude to other currents involved in the computations, suggesting that it may be significant \&ndash; at least in parts of the simulation. The magnitude of the error introduced in the membrane potential is several millivolts, and this error also translates into errors in the predicted extracellular potentials. While the error becomes negligible if we assume the extracellular conductivity to be very large, this assumption is, unfortunately, not easy to justify a priori for all situations of interest.},
	issn = {1662-5188},
	doi = {10.3389/fncom.2017.00027},
	url = {http://journal.frontiersin.org/article/10.3389/fncom.2017.00027},
	author = {Tveito, Aslak and Karoline Horgmo {J{\ae}ger} and Glenn T. {Lines} and Paszkowski, {\L}ukasz and Sundnes, Joakim and Andrew G {Edwards} and M{\"a}ki-Marttunen, Tuomo and Halnes, Geir and Gaute T {Einevoll}}
}
@article {25219,
	title = {Ion diffusion may introduce spurious current sources in Current-Source Density (CSD) analysis},
	journal = {Journal of Neurophysiology},
	volume = {118},
	year = {2017},
	pages = {114-120},
	publisher = {{Am Physiological Soc},
	doi = {10.1152/jn.00976.2016},
	author = {Halnes, Geir and M{\"a}ki-Marttunen, Tuomo and Klas H {Pettersen} and Ole A {Andreassen} and Gaute T {Einevoll}}
}
@article {25217,
	title = {Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue},
	journal = {PLOS Computational Biology},
	volume = {12},
	number = {11},
	year = {2016},
	pages = {e1005193},
	publisher = {PLoS},
	author = {Halnes, Geir and M{\"a}ki-Marttunen, Tuomo and Keller, Daniel and Klas H. {Pettersen} and Ole A. {Andreassen} and Gaute T {Einevoll}}
}
@article {25212,
	title = {Functional Effects of Schizophrenia-Linked Genetic Variants on Intrinsic Single-Neuron Excitability: A Modeling Study},
	journal = {Biological Psychiatry: Cognitive Neuroscience and Neuroimaging},
	volume = {1},
	year = {2016},
	pages = {49-59},
	publisher = {Elsevier},
	author = {M{\"a}ki-Marttunen, Tuomo and Halnes, Geir and Devor, Anna and Witoelar, Aree and Bettella, Francesco and Djurovic, Srdjan and Wang, Yunpeng and Gaute T {Einevoll} and Ole A. {Andreassen} and Anders M {Dale}}
}
